Dear Eleanor,
Yes, difference maps are weighted by FOM, with the coefficient being m*Fo-D*Fc,
phased by the model. If Fc is small, then m will be small because, even if Fo
is large, you have no idea what phase to assign to the difference. If Fc is
large because you haven't treated bulk solvent
This is hunch speak - not proper analysis, but it is possible to get huge
Fcalc, and hence large difference map terms, at low resolution by assuming
the solvent volume is a vacuum, not full of partially ordered water
molecules.
The Babinet scaling can do something to correct this but it is a very
>>And as we often end our beer-discussions - may be all protein space groups
>>are actually true P1, just close enough to satisfy the high symmetry rules ..
>>but this is getting a bit philosophical I know ..
Could we add that all crystals are twinned, just some are in such a way as to
be a pro
Dear all,
regarding the "remaining strong differences" between measured data and
calculated SFs from a a finished (high res structure) I once investigated a
bit into this going back to images and looking up some extreme outliers.
I found the same - those were clear strong diffraction spots, not ice
James,
Where we diverge is with your interpretation that big differences lead to small
FOMs. The size of the FOM depends on the product of Fo and Fc, not their
difference. The FOM for a reflection where Fo=1000 and Fc=10 is very different
from the FOM for a reflection with Fo=5000 and Fc=4010
esting map.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von James Holton
Gesendet: Mittwoch, 16. Oktober 2019 17:02
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Figure of merit in refinement
EXTERNAL : Real sender is
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@j
All very true Randy,
But nevertheless every hkl has an FOM assigned to it, and that is used
to calculate the map. Statistical distribution or not, the trend is
that hkls with big amplitude differences get smaller FOMs, so that means
large model-to-data discrepancies are down-weighted. I wond
Hi Fellows,
I have tried to summarize these issues James raised,
in consistent notation in Chapter 12 of BMC of which you can download an
excerpt here:
https://www.dropbox.com/s/crzwoa5lb8bk3x5/Pages_611-619_from%20BMC_rupp_ch12.pdf?dl=0
> if your R factor is 55% then your phases probably are
Hi James,
I'm sure you realise this, but it's important for other readers to remember
that the FOM is a statistical quantity: we have a probability distribution for
the true phase, we pick one phase (the "centroid" phase that should minimise
the RMS error in the density map), and then the FOM i
James - you do the most sensible informative tests! Thank you..
Eleanor
On Fri, 4 Oct 2019 at 16:39, James Holton wrote:
> I've done a few little experiments over the years using simulated data
> where I know the "correct" phase, trying to see just how accurate FOMs
> are. What I have found in
I've done a few little experiments over the years using simulated data
where I know the "correct" phase, trying to see just how accurate FOMs
are. What I have found in general is that overall FOM values are fairly
well correlated to overall phase error, but if you go
reflection-by-reflection t
Thank you, Eleanor, for an important reminder :
obviously, one more recent and relevant paper is that by Read and McCoy (Acta
Cryst, D, 2016)
[ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784668/ |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784668/ ]
With best wishes,
Sacha
- L
The maths for estimating the FOM during refinement in REFMAC is
given in some detail in the original paper.
However the assessment uses estimates of the observation standard
uncertainly, and SigmaA - the estimate of the resolution dependent
error due to coordinate errors and missing atoms -
and
Dear Andre,
I would strongly advice you to look at the article by Lunin and Skovoroda (Acta
Cryst, A, 1995) that addresses exactly your question:
[ https://scripts.iucr.org/cgi-bin/paper?vs0124 |
https://scripts.iucr.org/cgi-bin/paper?vs0124 ]
The authors remind a very important point that
Dear Jonathan, many thanks for this. I will have a look at it right away.
With best wishes,
Andre.
On Wed, Oct 2, 2019, 7:51 PM Jonathan Cooper wrote:
> This is a very good place to start:
>
> https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html
>
> Also recommend this one:
>
>
This is a very good place to start:
https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html
Also recommend this one:
https://doi.org/10.1107/S0108767386099622
and Main, P. (1979) Acta Cryst. A35, 779-85 - the maths in this one are a bit
easier!
On Wednesday, 2 October 2019,
Dear all,
How is the phase error estimated for any given reflection, specifically in
the context of model refinement? In terms of math I mean.
How useful is FOM in assessing the phase quality, when not for initial
experimental phases?
Many thank in advance,
Andre.
#
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